Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: ELF1

Gene summary for ELF1

Gene summary.

Gene information	Species	Human
	Gene symbol	ELF1
	Gene ID	1997
	Gene name	E74 like ETS transcription factor 1
	Gene Alias	EFTUD1
	Cytomap	13q14.11
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	P32519

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
1997	ELF1	CA_HPV_1	Human	Cervix	CC	3.96e-06	-9.21e-02	0.0264
1997	ELF1	CA_HPV_3	Human	Cervix	CC	8.48e-03	-4.96e-02	0.0414
1997	ELF1	CCI_1	Human	Cervix	CC	1.92e-05	7.78e-01	0.528
1997	ELF1	CCI_2	Human	Cervix	CC	5.24e-09	1.49e+00	0.5249
1997	ELF1	CCI_3	Human	Cervix	CC	9.46e-10	1.14e+00	0.516
1997	ELF1	Tumor	Human	Cervix	CC	2.36e-08	-3.48e-01	0.1241
1997	ELF1	sample3	Human	Cervix	CC	2.86e-09	-3.39e-01	0.1387
1997	ELF1	T1	Human	Cervix	CC	1.15e-05	-4.14e-01	0.0918
1997	ELF1	T3	Human	Cervix	CC	1.37e-10	-3.30e-01	0.1389
1997	ELF1	HTA11_3410_2000001011	Human	Colorectum	AD	5.32e-27	-6.61e-01	0.0155
1997	ELF1	HTA11_347_2000001011	Human	Colorectum	AD	3.80e-02	3.39e-01	-0.1954
1997	ELF1	HTA11_3361_2000001011	Human	Colorectum	AD	1.50e-03	-5.59e-01	-0.1207
1997	ELF1	HTA11_5212_2000001011	Human	Colorectum	AD	1.64e-02	-3.04e-01	-0.2061
1997	ELF1	HTA11_7862_2000001011	Human	Colorectum	AD	1.44e-03	-3.77e-01	-0.0179
1997	ELF1	HTA11_866_3004761011	Human	Colorectum	AD	3.44e-09	-5.56e-01	0.096
1997	ELF1	HTA11_7696_3000711011	Human	Colorectum	AD	1.19e-02	-3.08e-01	0.0674
1997	ELF1	HTA11_6818_2000001021	Human	Colorectum	AD	2.32e-03	-4.75e-01	0.0588
1997	ELF1	HTA11_99999965104_69814	Human	Colorectum	MSS	6.66e-14	9.84e-01	0.281
1997	ELF1	HTA11_99999974143_84620	Human	Colorectum	MSS	4.11e-13	-5.18e-01	0.3005
1997	ELF1	A001-C-207	Human	Colorectum	FAP	1.39e-04	-3.67e-01	0.1278

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:000640211	Liver	Cirrhotic	mRNA catabolic process	109/4634	232/18723	1.30e-13	1.09e-11	109
GO:000038011	Liver	Cirrhotic	alternative mRNA splicing, via spliceosome	43/4634	77/18723	5.31e-09	2.10e-07	43
GO:190331311	Liver	Cirrhotic	positive regulation of mRNA metabolic process	56/4634	118/18723	7.05e-08	2.14e-06	56
GO:004348811	Liver	Cirrhotic	regulation of mRNA stability	69/4634	158/18723	1.44e-07	3.87e-06	69
GO:004348711	Liver	Cirrhotic	regulation of RNA stability	73/4634	170/18723	1.44e-07	3.87e-06	73
GO:006101311	Liver	Cirrhotic	regulation of mRNA catabolic process	70/4634	166/18723	5.91e-07	1.30e-05	70
GO:000038111	Liver	Cirrhotic	regulation of alternative mRNA splicing, via spliceosome	31/4634	60/18723	6.48e-06	1.02e-04	31
GO:003424911	Liver	Cirrhotic	negative regulation of cellular amide metabolic process	100/4634	273/18723	7.34e-06	1.13e-04	100
GO:006115711	Liver	Cirrhotic	mRNA destabilization	38/4634	84/18723	3.34e-05	4.13e-04	38
GO:005077911	Liver	Cirrhotic	RNA destabilization	39/4634	88/18723	4.69e-05	5.47e-04	39
GO:006101411	Liver	Cirrhotic	positive regulation of mRNA catabolic process	38/4634	87/18723	8.55e-05	9.25e-04	38
GO:001714811	Liver	Cirrhotic	negative regulation of translation	87/4634	245/18723	1.01e-04	1.05e-03	87
GO:00002454	Liver	Cirrhotic	spliceosomal complex assembly	34/4634	79/18723	2.78e-04	2.46e-03	34
GO:003526411	Liver	Cirrhotic	multicellular organism growth	47/4634	132/18723	3.40e-03	1.89e-02	47
GO:00063762	Liver	Cirrhotic	mRNA splice site selection	20/4634	49/18723	9.60e-03	4.35e-02	20
GO:002261322	Liver	HCC	ribonucleoprotein complex biogenesis	355/7958	463/18723	7.76e-52	4.92e-48	355
GO:000838022	Liver	HCC	RNA splicing	313/7958	434/18723	1.36e-36	1.73e-33	313
GO:000989622	Liver	HCC	positive regulation of catabolic process	335/7958	492/18723	3.83e-31	1.87e-28	335
GO:003133122	Liver	HCC	positive regulation of cellular catabolic process	295/7958	427/18723	3.20e-29	1.45e-26	295
GO:004427021	Liver	HCC	cellular nitrogen compound catabolic process	303/7958	451/18723	9.76e-27	3.64e-24	303

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

ELF1

SNV

Missense_Mutation

c.151N>G

p.Leu51Val

p.L51V

P32519

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-BH-A0B4-01

Breast

breast invasive carcinoma

Male

>=65

III/IV

Hormone Therapy

tamoxiphen

ELF1

SNV

Missense_Mutation

c.1248N>C

p.Gln416His

p.Q416H

P32519

protein_coding

tolerated(0.36)

possibly_damaging(0.759)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

ELF1

SNV

Missense_Mutation

c.133N>G

p.Leu45Val

p.L45V

P32519

protein_coding

deleterious(0.02)

possibly_damaging(0.678)

TCGA-BH-A0H5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

ELF1

SNV

Missense_Mutation

novel

c.740N>T

p.Ser247Phe

p.S247F

P32519

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

ELF1

SNV

Missense_Mutation

c.1685N>G

p.Thr562Arg

p.T562R

P32519

protein_coding

deleterious(0.04)

benign(0.136)

TCGA-D8-A1XQ-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ELF1

insertion

Frame_Shift_Ins

novel

c.101_102insT

p.Ile35AsnfsTer9

p.I35Nfs*9

P32519

protein_coding

TCGA-A8-A08L-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

ELF1

SNV

Missense_Mutation

rs766946264

c.1472C>T

p.Ala491Val

p.A491V

P32519

protein_coding

tolerated(0.34)

benign(0.011)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ELF1

SNV

Missense_Mutation

rs747465409

c.371T>C

p.Ile124Thr

p.I124T

P32519

protein_coding

tolerated(0.05)

benign(0.165)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ELF1

SNV

Missense_Mutation

c.1397N>G

p.Phe466Cys

p.F466C

P32519

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ELF1

SNV

Missense_Mutation

novel

c.700G>A

p.Glu234Lys

p.E234K

P32519

protein_coding

deleterious(0)

probably_damaging(0.962)

TCGA-HM-A4S6-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID

Symbol

Category

Interaction Types

Drug Claim Name

Drug Name

PMIDs

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